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This retrospective study aims to identify and describe the problems associated with the laboratory and clinical diagnosis of leptospirosis. A total of 4,813 patients with suspected leptospirosis from an area of the Czech Republic, with a total population of 1.15 million, were examined during the period 2002-2010. Our study included only 855 patients: 545 men (mean age 41.03 ± 19.24) and 310 women (mean age 41.47 ± 20.3) who were examined using microscopic agglutination test (MAT) and a polymerase chain reaction (PCR). All patients and their physicians filled in questionnaires, which included anamnestic data, clinical symptoms and the results of laboratory tests. Out of total suspected, 89 patients (1.85%), tested positive for leptospirosis, of which 50 have been examined only serologically by MAT. Of 855 patients in our study undergoing both PCR and MAT tests, 39 have tested positive for leptospirosis. The most frequent symptom in patients with leptospirosis included fever (91.6%) and headache (69.4%). The correct laboratory diagnosis of leptospirosis depends on biological material being tested before the start of antibiotic treatment, since leptospires are extremely sensitive to antibiotics. Consequently, the PCR results alone may produce a false negative result after 24 hours following treatment with antibiotics. [ABSTRACT FROM AUTHOR]